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Title:Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies
Authors:ID Soler, Miguel, SISSA (Author)
ID De Marco, Ario, UNG (Author)
ID Fortuna, Sara, UNG (Author)
Files:.pdf Soler_et_al-2016-Scientific_Reports.pdf (1,95 MB)
MD5: 8FFF6923296A39E23851D624572720B9
 
Language:English
Work type:Not categorized
Typology:1.01 - Original Scientific Article
Organization:UNG - University of Nova Gorica
Abstract:Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and wholemolecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules
Keywords:nanobodies, molecular dynamics, modeling, antibody solubility
Publication version:Version of Record
Year of publishing:2016
Number of pages:11
Numbering:6:34869 |
PID:20.500.12556/RUNG-2698 New window
COBISS.SI-ID:4531707 New window
DOI:10.1038/srep34869 New window
NUK URN:URN:SI:UNG:REP:LFCPDQKV
Publication date in RUNG:11.10.2016
Views:5866
Downloads:249
Metadata:XML DC-XML DC-RDF
:
SOLER, Miguel, DE MARCO, Ario and FORTUNA, Sara, 2016, Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies. Scientific Reports [online]. 2016. Vol. 6:34869 |. [Accessed 21 April 2025]. DOI 10.1038/srep34869. Retrieved from: https://repozitorij.ung.si/IzpisGradiva.php?lang=eng&id=2698
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Record is a part of a journal

Title:Scientific Reports
Publisher:Springer Nature Publishing
Year of publishing:2016

Document is financed by a project

Funder:ARRS - Slovenian Research Agency
Project number:N4-0046

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
Licensing start date:11.10.2016

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